Genome Structure

Time required for half-renaturation is directly proportional to sequence complexity

• For a renaturation measurement, one usually shears DNA to a constant fragment length L (e.g. 400 bp). Then L is no longer a variable, and

• E.g. E. coli N = 4.639 x 106 bp

• (4)

• (5)

• (6)

Types of DNA in each kinetic component

• Fig. 1.7.5

• Human genomic DNA

Clustered repeated sequences

• Human
• chromosomes,
• ideograms
• G-bands

• Tandem repeats on
• every chromosome:
• Telomeres
• Centromeres

• 5 clusters of repeated rRNA genes:
• Short arms of chromosomes 13, 14, 15, 21, 22

Almost all transposable elements in mammals fall into one of four classes

Short interspersed repetitive elements: SINEs

• Example: Alu repeats
• Most abundant repeated DNA in primates
• Short, about 300 bp
• About 1 million copies
• Likely derived from the gene for 7SL RNA
• Cause new mutations in humans
• They are retrotranposons
• DNA segments that move via an RNA intermediate.
• MIRs: Mammalian interspersed repeats
• SINES found in all mammals
• Analogous short retrotransposons found in genomes of all vertebrates.

Long interspersed repetitive elements: LINEs

• Moderately abundant, long repeats
• LINE1 family: most abundant
• Up to 7000 bp long
• About 50,000 copies
• Retrotransposons
• Encode reverse transcriptase and other enzymes required for transposition
• No long terminal repeats (LTRs)
• Cause new mutations in humans
• Homologous repeats found in all mammals and many other animals

Other common interspersed repeated sequences in humans

• LTR-containing retrotransposons
• MaLR: mammalian, LTR retrotransposons
• Endogenous retroviruses
• MER4 (MEdium Reiterated repeat, family 4)
• Repeats that resemble DNA transposons
• MER1 and MER2
• Mariner repeats
• Were active early in mammalian evolution but are now inactive

Finding repeats

• Compare a sequence to a database of known repeat sequences from the organism of interest
• RepeatMasker
• Arian Smit and P. Green, U. Wash.
• http://ftp.genome.washington.edu/cgi-bin/RepeatMasker
• Try it on INS gene sequence